From 922b3949afc188644776b70acb8a1363f640f610 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 16 Feb 2015 10:18:40 +0100
Subject: [PATCH] Open and close handlers properly
---
.../nl/lumc/sasc/biopet/tools/FastqSync.scala | 30 +++++++++++--------
1 file changed, 18 insertions(+), 12 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
index c01ddf388..5096bdea8 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala
@@ -165,8 +165,6 @@ object FastqSync extends ToolCommand {
}
syncIter(pre.iterator.asScala.toStream, seqA.iterator.asScala.toStream, seqB.iterator.asScala.toStream)
- seqOutA.close()
- seqOutB.close()
(numDiscA, numDiscB, numKept)
}
@@ -252,15 +250,23 @@ object FastqSync extends ToolCommand {
val commandArgs: Args = parseArgs(args)
- val (numDiscA, numDiscB, numKept) = syncFastq(
- new FastqReader(commandArgs.refFastq),
- new FastqReader(commandArgs.inputFastq1),
- new FastqReader(commandArgs.inputFastq2),
- new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq1), 3000),
- new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq2), 3000))
-
- println(s"Filtered $numDiscA reads from first read file.")
- println(s"Filtered $numDiscB reads from second read file.")
- println(s"Synced files contain $numKept reads.")
+ val refReader = new FastqReader(commandArgs.refFastq)
+ val AReader = new FastqReader(commandArgs.inputFastq1)
+ val BReader = new FastqReader(commandArgs.inputFastq2)
+ val AWriter = new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq1), 3000)
+ val BWriter = new AsyncFastqWriter(new BasicFastqWriter(commandArgs.outputFastq2), 3000)
+
+ try {
+ val (numDiscA, numDiscB, numKept) = syncFastq(refReader, AReader, BReader, AWriter, BWriter)
+ println(s"Filtered $numDiscA reads from first read file.")
+ println(s"Filtered $numDiscB reads from second read file.")
+ println(s"Synced files contain $numKept reads.")
+ } finally {
+ refReader.close()
+ AReader.close()
+ BReader.close()
+ AWriter.close()
+ BWriter.close()
+ }
}
}
--
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